Rainbow trout is one of the widely used aquaculture species for food worldwide. Due to its commercial importance, various genomic resources are available for the trout including a draft reference genome, microRNA repertoire, quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with different production traits. However, many of these genomic resources still need improvement in terms of quality and quantity. The only available genome draft is not completely annotated, and lacks non-coding RNA and some protein coding genes. Similarly, majority of the previous work aimed at identification of trait-associated genetic markers were not robust due to limitation of genomic resources that were previously available.